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Cookiecutter specifications

Information


Unique identifier OMICS_09649
Name Cookiecutter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Cookiecutter takes as input one or several FASTQ files or one or several pairs of FASTQ files and requires a file with a list of k-mers for filtering.
Operating system Unix/Linux, Mac OS
Programming languages C++
Computer skills Advanced
Stability Stable
Requirements
Make, gcc, Python
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Aleksey Komissarov <>

Publication for Cookiecutter

Cookiecutter citations

 (9)
library_books

Assembly of the Boechera retrofracta Genome and Evolutionary Analysis of Apomixis Associated Genes

2018
PMCID: 5924527
PMID: 29597328
DOI: 10.3390/genes9040185

[…] libraries and sequencing were performed following lee et al []., filtration of the pe library lib400 was performed in two stages. first, reads containing long adapter fragments were removed using cookiecutter []. then trimmomatic [] was used to filter out reads with short adapter fragments. however, according to the discovar requirements no trimming or quality filtration was performed […]

library_books

Clustergrammer, a web based heatmap visualization and analysis tool for high dimensional biological data

2017
PMCID: 5634325
PMID: 28994825
DOI: 10.1038/sdata.2017.151

[…] visualizations within shareable jupyter notebooks. the clustergrammer-widget utilizes the core clustergrammer-js and clustergrammer-py libraries. clustergrammer-widget was built using the widget-cookiecutter template (https://github.com/jupyter-widgets/widget-cookiecutter). clustergrammer-widget can be installed using pip (https://pypi.python.org/pypi/clustergrammer_widget) and the source […]

library_books

A unique Cretaceous–Paleogene lineage of piranha jawed pycnodont fishes

2017
PMCID: 5533729
PMID: 28754956
DOI: 10.1038/s41598-017-06792-x

[…] might also have developed a facultative ectoparasitic foraging strategy consisting of biting fins of large animals, like in some modern fishes with a specialized cutting dentition (i.e., cookiecutter sharks and piranhas; figs  and and ; see supplementary text , part g). butterfly, eagle and devil rays (gymnuridae, myliobatidae and mobulidae, respectively), whale sharks […]

library_books

The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

2016
PMCID: 4835728
PMID: 27089831
DOI: 10.1038/srep24501

[…] using “trim galore!” software (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with default parameters. we then cleaned out reads containing 23-mer illumina-specific primers using cookiecutter (https://pypi.python.org/pypi/cookiecutter/0.7.2)., the cleaned reads from the microdissected chromosomes were mapped to the three assembled asian arowana genomes (golden, red and green) […]

library_books

Chromosomal Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi layered Scaffolding

2016
PMCID: 4833346
PMID: 27082250
DOI: 10.1371/journal.pgen.1005954

[…] as well as the repeats present in repbase []., we used the jellyfish software [] for computing 23-mer frequencies and choosing a subset of 23-mers with coverage greater than 1,000. we used the cookiecutter package [] for extraction of raw reads containing subset of 23-mers with coverage greater than 1000. the selected reads were used to manually assemble tandem repeat monomer consensus […]

library_books

Anti apoptotic genes are synergistically activated in OVSAYO cells cultured under conditions of serum starvation and hypoxia

2015
PMCID: 4583649
PMID: 26484240
DOI: 10.1016/j.gdata.2015.05.029

[…] slides were scanned using an agilent dna microarray scanner and data were processed using agilent feature extraction 7 software. feature and background regions were determined using the cookiecutter segmentation algorithm to obtain processed signal intensities. background was subtracted (spatial detrending) and then, signal intensity of total array was corrected (multiplicative […]


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Cookiecutter institution(s)
Bioinformatics Institute, St. Petersburg, Russia; Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia; Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, Oceanographic Center, Nova Southeastern University Ft Lauderdale, Ft Lauderdale, FL, USA

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